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Two-dimensional (2D) systems with time-dependent controls admit a quadratic Hamiltonian modeling near potential minima. Independent, dynamical normal modes facilitate inverse Hamiltonian engineering to control the system dynamics, but some systems are not separable into independent modes by a point transformation. For these "coupled systems" 2D invariants may still guide the Hamiltonian design. The theory to perform the inversion and two application examples are provided: (i) We control the deflection of wave packets in transversally harmonic wave guides and (ii) we design the state transfer from one coupled oscillator to another.